ProjectSummary Viralresistanceisessentialinallkingdomsoflife,althoughdiverseorganismshave evolvedequallydiversemechanismsforcombattinginfection.Inbacteriaandarchaea,the CRISPR(clusteredregularlyinterspacedshortpalindromicrepeats)adaptiveimmunesystem clearsinvadingDNAduringinfectionthroughasmall-RNAguidedinterferencemechanism. CRISPRimmunityproceedsthroughtwostages:adaptation,inwhichfragmentsofinvasive DNAfrombacteriophagesorplasmidsareinsertedasspacerswithintheCRISPRlocusofthe hostgenomeandsubsequentlyserveastemplatesfortheproductionofsmallguideCRISPR (cr)RNAs;?andinterference,duringwhichthecrRNAanditseffectorCRISPRassociated(Cas) proteinsbindcomplementarytargetregionsoftheinvadingDNA,leadingtoitsdestructionbya Casendonuclease.Ourgoalistodefinehowbacteriamaximizetheirimmunecapacitytogain anadvantageinthemoleculararmsraceagainsttheirinvaders.Ourfirstgoalistounderstand thesequence-dependenceofimmunesystemevasionthroughthedevelopmentofpoint mutationswithintheinvadingDNA.Ourpreviousstudieshaverevealedthatspacersequence greatlyinfluencestheeffectivenessofthese?escape?mutations,suggestingforthefirsttime thatsomespacersequencesprovidestrongerimmunitythanothers.Inaddition,wehave discoveredthatduringinitialinfection,bacteriauseatwo-tiereddefensivesystemtobroaden theiradaptationcapacity.Wewillevaluatetheimpactofthistacticonhostimmunityand elucidatethemolecularmechanismsunderlyingthisdefensestrategy.Finally,wewilldetermine thestructuralbasisforrapidadaptationtriggeredwhentheCRISPRmachinerysensesnon- canonicaltargetsequences.Ourstudieswillhavemajorimplicationsontheunderstandingof host-virusinteractionsandco-evolution,animportantdeterminantofthecompositional dynamicswithincomplexecologicalsystemsincludingthehumanmicrobiome.